I noticed this too. Didn't say anything about it because it always happened when I was importing a map from SPWW2 into MBT. I therefore assumed it might simply be a compatibility issue specific to SPWW2.
I've noticed that loading the "autosave" version of a map you have worked on ("bombed", in this case) using the dedicated map editor tool once you are actually building the scenario itself (purchasing units etc.) seems to be another way to get around this problem.
Another thing I've noticed is that when you buy new units in the scenario editor after you've deployed some units already in a manner where they face in any direction other than the default left or right (depending on p1 and p2 "facing" settings, of course) this then leads to all the units facing in the default direction again when you go back to deploy the new additions.
No idea if this is a bug though.

This is why I buy all my units, set them up, then align them. They don't reset unless you buy more units, I've come to find out.

This has been a LONG standing SP issue and one that has bit me a time or two as well so it's on the " look into it" list for next year. The "secret" is to NOT face your units until you are CERTAIN you have all you need on both sides.....THEN face the unit and make a final save and above all resist the urge to "tinker"